Hello Diego-- > I am working with XPLOR-NIH adding CrioEM density map > potentials during the calculation. Due to my system is a symmetric > oligomer, I am working > also with NCS condition (turning on the flags PVDW and PELE). > I would like to ask you if is also possible to turn on the Density Map > Energy term for the NCS images of my molecule (v.g. as the flag PDVW > and PELE but for the density map energy term)?
The short answer is "no," but please see the last paragraph. Presumably your map corresponds to the complete oligomer, so that the density map for the entire construct must be used. It is possible that the density map might be more quickly generated by using the symmetry operators, but this is not yet implemented. Do note: PVDW and PELE work with strict symmetry facility in the old XPLOR interface. It is not clear to me that using electrostatics is a good idea- so please be careful with that. To be completely clear, when using strict symmetry the coordinates of a single subunit are explicitly represented, and the coordinates of the other oligomer subunits are generated using symmetry operations. The advantage of this approach is that there are fewer coordinates positions to determine, and one doesn't have to worry about symmetry restraints or their associated energies. You can use strict symmetry within Xplor-NIH's Python interface using the symSimulation facility. This supports all of the native Python energy terms including the density map term, and the RepelPot term for purely repulsive interactions. There is an example of its use in python/tests/symSimulation.py in the Xplor-NIH distribution. It seems I haven't gotten around to writing documentation, though, so please bug me if you'd like to use this, and I'll pull things together. best regards-- Charles _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
